[gmx-users] Unable to write whole trajectory with trjconv and error in gmx check

[Dasgupta, R.]

Dear All,

I am facing problem with GROMACS version 2016.1 and 2016.3. I gave a run of 30ns of my protein in our local cluster that uses sbatch to queue the job. My input file for the sbatch is the following:


#!/bin/bash

#SBATCH -t 5-00:00:00

#SBATCH -N 4

#SBATCH --ntasks-per-node=12


export GMX_MAXBACKUP=-1 (this is required because of multiple backup files gromacs makes)


srun -n 4 /home/dasgupta/gromacs/bin/gmx mdrun -v -deffnm 2my9_nseed


Everything went smoothly neither the .out file did not show any error nor the .log file did not show any inconsistency. The problem started when I used gmx trjconv to extract the trajectory and make the .pdb file for visualisation. After just 1ns it was unable to write any other frames. So, I tried to check the trajectory file by the following command:


gmx check -f xxx.trr


This is the error I got:


Program:     gmx check, version 2016.3

Source file: src/gromacs/fileio/trrio.cpp (line 114)


Fatal error:

Failed to find GROMACS magic number in trr frame header, so this is not a trr

file!


Before this error there was this output (just a portion of the output is shown here):


Timesteps at t=1159 don't match (1, 9)


Timesteps at t=1168 don't match (9, 1)


Timesteps at t=1170 don't match (1, -7)


Timesteps at t=1163 don't match (-7, 1)


Timesteps at t=1165 don't match (1, 9)


Timesteps at t=1174 don't match (9, 1)

Reading frame    1200 time 1183.000

Timesteps at t=1183 don't match (1, -7)


Timesteps at t=1176 don't match (-7, 1)


Timesteps at t=1179 don't match (1, 4)


Timesteps at t=1183 don't match (4, 1)


Timesteps at t=1186 don't match (1, 3)


Timesteps at t=1189 don't match (3, 1)

Warning at frame 1211: coordinates for atom 1390 are large (7.68295e+31)

Warning at frame 1211: coordinates for atom 1391 are large (2.75578e+23)

Warning at frame 1211: there are 4 particles with all coordinates zero


I will appreciate if anyone can help me in solving this problem.


Thank you very much in advance.


Rubin Dasgupta,

Phd Student,

Leiden University,

The Netherlands.